I'll limit myself to 5 from each side:
Confederate:
Robert E. Lee - after Day 1 he should have not attacked. Twice. Forming a defensive line at South Mountain and waiting for Meade, or even better, letting Ewell attack a defenseless Harrisburg as requested, and cross the Susquehanna with the whole ANV days ahead of the Federals, up there (and with the Wrightsville bridge burned) would have been the way to go.
James J. Archer - Even Davis, with one less regiment bettered him in Day 1. Running, trying to hide and getting arrested in a thicket by a private, is not befit to a general. But he was a political general.
Alfred Iverson Jr. - Too drunk to fight? Who knows. But a brigadier General does not let his brigade to go to battle alone, even a political one.
John M. Brockenbrough - Too sad to fight? He lost his brother at day 1 and during Pickett's charge he let his (Heth's) brigade go on without him. No wonder they went only half way before they ran back. Heth's Brigade, thus, (Col. Robert Murphy Mayo of the 47th VA commanding,)makes the list as well... Another political general adverse to fighting. Must be a theme here.
Union:
Alexander Schimmelfennig - Spending the whole battle in someone's outhouse is not good generalship. Esp. for someone who was supposedly a seasoned Prussian soldier.
Francis C. Barlow - No idea how they named a hill after him or why he even got to command a Division. First General going to battle exposing his own flank. Another Lawyer made general.
O O Howard - Probably made the second biggest mistake in the Battle (after Lee,) which he was lucky not to have any consequences: He kept sending troops from the 11th Corps up North, until there was a single brigade left in support of Cemetery Hill. Saved by the clock, Slocum's arrival, and the fact that when Pender's Confederates turned the Iron Brigade around at the Seminary Ridge, they decided to follow them through town, instead of going to the High Ground.
I Corps and XI Corps. That was not quite textbook retreat. Makes Heth's Brigade who went half way look like soldiers...